Zinc in PDB 2rb4: Crystal Structure of the Helicase Domain of Human DDX25 Rna Helicase

The structure of Crystal Structure of the Helicase Domain of Human DDX25 Rna Helicase, PDB code: 2rb4 was solved by L.Lehtio, M.Hogbom, J.Uppenberg, C.H.Arrowsmith, H.Berglund, A.M.Edwards, M.Ehn, S.Flodin, A.Flores, S.Graslund, B.M.Hallberg, M.Hammarstrom, T.Kotenyova, P.Nilsson-Ehle, P.Nordlund, T.Nyman, D.Ogg, C.Persson, J.Sagemark, P.Stenmark, M.Sundstrom, A.G.Thorsell, S.Van Den Berg, J.Weigelt, L.Holmberg-Schiavone, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.44 / 2.80
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	70.310, 70.310, 187.120, 90.00, 90.00, 90.00
R / Rfree (%)	23.3 / 26.7

The structure of Crystal Structure of the Helicase Domain of Human DDX25 Rna Helicase also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of the Helicase Domain of Human DDX25 Rna Helicase (pdb code 2rb4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Crystal Structure of the Helicase Domain of Human DDX25 Rna Helicase, PDB code: 2rb4:

Zinc binding site 1 out of 1 in the Crystal Structure of the Helicase Domain of Human DDX25 Rna Helicase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Helicase Domain of Human DDX25 Rna Helicase within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn481 b:84.9 occ:1.00 SG A:CYS398 2.3 84.6 1.0 SG B:CYS398 2.3 82.1 1.0 ND1 A:HIS430 2.6 75.8 1.0 CB A:CYS398 3.0 83.3 1.0 CB B:CYS398 3.1 82.3 1.0 CE1 A:HIS430 3.3 76.3 1.0 ND1 B:HIS430 3.4 78.4 1.0 CB B:ARG400 3.6 84.2 1.0 CG A:HIS430 3.7 77.5 1.0 CE1 B:HIS430 4.1 78.7 1.0 CB A:ARG400 4.2 84.2 1.0 CB A:HIS430 4.2 78.7 1.0 CD B:ARG400 4.3 82.9 1.0 CA B:CYS398 4.3 82.2 1.0 N B:ARG400 4.4 83.9 1.0 NE2 A:HIS430 4.5 75.1 1.0 CA A:CYS398 4.5 83.3 1.0 C B:CYS398 4.5 82.1 1.0 CG B:HIS430 4.6 78.7 1.0 O B:CYS398 4.6 81.7 1.0 CG B:ARG400 4.6 83.4 1.0 CA B:ARG400 4.7 84.1 1.0 CD2 A:HIS430 4.7 75.9 1.0 CD A:ARG400 4.8 83.1 1.0 N A:ARG400 4.8 83.9 1.0 CB B:HIS430 4.9 78.9 1.0 C A:CYS398 4.9 83.1 1.0 N B:ALA399 5.0 82.6 1.0

P.Schutz, T.Karlberg, S.Van Den Berg, R.Collins, L.Lehtio, M.Hogbom, L.Holmberg-Schiavone, W.Tempel, H.W.Park, M.Hammarstrom, M.Moche, A.G.Thorsell, H.Schuler. Comparative Structural Analysis of Human Dead-Box Rna Helicases. Plos One V. 5 12791 2010.
ISSN: ESSN 1932-6203
PubMed: 20941364
DOI: 10.1371/JOURNAL.PONE.0012791